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    Mungall, Chris

    TitleComputer Scientist
    SchoolLawrence Berkeley National Lab
    DepartmentEnviron Genomics & Systems Bio
    Address1 Cyclotron Road
    Berkeley CA 94720
    Phone510/486-4170
    vCardDownload vCard

      Collapse Bibliographic 
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      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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      1. de Rie D, Abugessaisa I, Alam T, Arner E, Arner P, Ashoor H, Åström G, Babina M, Bertin N, Burroughs AM, Carlisle AJ, Daub CO, Detmar M, Deviatiiarov R, Fort A, Gebhard C, Goldowitz D, Guhl S, Ha TJ, Harshbarger J, Hasegawa A, Hashimoto K, Herlyn M, Heutink P, Hitchens KJ, Hon CC, Huang E, Ishizu Y, Kai C, Kasukawa T, Klinken P, Lassmann T, Lecellier CH, Lee W, Lizio M, Makeev V, Mathelier A, Medvedeva YA, Mejhert N, Mungall C, Noma S, Ohshima M, Okada-Hatakeyama M, Persson H, Rizzu P, Roudnicky F, Sætrom P, Sato H, Severin J, Shin JW, Swoboda RK, Tarui H, Toyoda H, Vitting-Seerup K, Winteringham L, Yamaguchi Y, Yasuzawa K, Yoneda M, Yumoto N, Zabierowski S, Zhang PG, Wells CA, Summers KM, Kawaji H, Sandelin A, Rehli M. An integrated expression atlas of miRNAs and their promoters in human and mouse. Nat Biotechnol. 2017 Sep; 35(9):872-878. PMID: 28829439.
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      2. Meehan TF, Conte N, West DB, Jacobsen JO, Mason J, Warren J, Chen CK, Tudose I, Relac M, Matthews P, Karp N, Santos L, Fiegel T, Ring N, Westerberg H, Greenaway S, Sneddon D, Morgan H, Codner GF, Stewart ME, Brown J, Horner N. Disease model discovery from 3,328 gene knockouts by The International Mouse Phenotyping Consortium. Nat Genet. 2017 Aug; 49(8):1231-1238. PMID: 28650483.
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      3. Osumi-Sutherland D, Courtot M, Balhoff JP, Mungall C. Dead simple OWL design patterns. J Biomed Semantics. 2017 Jun 05; 8(1):18. PMID: 28583177.
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      4. Elhanan G, Ochs C, Mejino JLV, Liu H, Mungall C, Perl Y. From SNOMED CT to Uberon: Transferability of evaluation methodology between similarly structured ontologies. Artif Intell Med. 2017 Jun; 79:9-14. PMID: 28532962.
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      5. Holmes IH, Mungall C. BioMake: a GNU Make-compatible utility for declarative workflow management. Bioinformatics. 2017 May 09. PMID: 28486579.
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      6. Mungall C, McMurry JA, Köhler S, Balhoff JP, Borromeo C, Brush M, Carbon S, Conlin T, Dunn N, Engelstad M, Foster E, Gourdine JP, Jacobsen JO, Keith D, Laraway B, Lewis SE, NguyenXuan J, Shefchek K, Vasilevsky N, Yuan Z, Washington N, Hochheiser H, Groza T, Smedley D, Robinson PN, Haendel MA. The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species. Nucleic Acids Res. 2017 Jan 04; 45(D1):D712-D722. PMID: 27899636.
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      7. Köhler S, Vasilevsky NA, Engelstad M, Foster E, McMurry J, Aymé S, Baynam G, Bello SM, Boerkoel CF, Boycott KM, Brudno M, Buske OJ, Chinnery PF, Cipriani V, Connell LE, Dawkins HJ, DeMare LE, Devereau AD, de Vries BB, Firth HV, Freson K, Greene D, Hamosh A, Helbig I, Hum C, Jähn JA, James R, Krause R, F Laulederkind SJ, Lochmüller H, Lyon GJ, Ogishima S, Olry A, Ouwehand WH, Pontikos N, Rath A, Schaefer F, Scott RH, Segal M, Sergouniotis PI, Sever R, Smith CL, Straub V, Thompson R, Turner C, Turro E, Veltman MW, Vulliamy T, Yu J, von Ziegenweidt J, Zankl A, Züchner S, Zemojtel T, Jacobsen JO, Groza T, Smedley D, Mungall C, Haendel M, Robinson PN. The Human Phenotype Ontology in 2017. Nucleic Acids Res. 2017 Jan 04; 45(D1):D865-D876. PMID: 27899602.
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      8. Lizio M, Harshbarger J, Abugessaisa I, Noguchi S, Kondo A, Severin J, Mungall C, Arenillas D, Mathelier A, Medvedeva YA, Lennartsson A, Drabløs F, Ramilowski JA, Rackham O, Gough J, Andersson R, Sandelin A, Ienasescu H, Ono H, Bono H, Hayashizaki Y, Carninci P, Forrest AR, Kasukawa T, Kawaji H. Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals. Nucleic Acids Res. 2017 Jan 04; 45(D1):D737-D743. PMID: 27794045.
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      9. Ong E, Xiang Z, Zhao B, Liu Y, Lin Y, Zheng J, Mungall C, Courtot M, Ruttenberg A, He Y. Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration. Nucleic Acids Res. 2017 Jan 04; 45(D1):D347-D352. PMID: 27733503.
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      10. Links AE, Draper D, Lee E, Guzman J, Valivullah Z, Maduro V, Lebedev V, Didenko M, Tomlin G, Brudno M, Girdea M, Dumitriu S, Haendel MA, Mungall C, Smedley D, Hochheiser H, Arnold AM, Coessens B, Verhoeven S, Bone W, Adams D, Boerkoel CF, Gahl WA, Sincan M. Distributed Cognition and Process Management Enabling Individualized Translational Research: The NIH Undiagnosed Diseases Program Experience. Front Med (Lausanne). 2016; 3:39. PMID: 27785453.
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      11. Buttigieg PL, Pafilis E, Lewis SE, Schildhauer MP, Walls RL, Mungall C. The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation. J Biomed Semantics. 2016 Sep 23; 7(1):57. PMID: 27664130.
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      12. Hill DP, D'Eustachio P, Berardini TZ, Mungall C, Renedo N, Blake JA. Modeling biochemical pathways in the gene ontology. Database (Oxford). 2016; 2016. PMID: 27589964; PMCID: PMC5009323.
      13. Smedley D, Schubach M, Jacobsen JOB, Köhler S, Zemojtel T, Spielmann M, Jäger M, Hochheiser H, Washington NL, McMurry JA, Haendel MA, Mungall C, Lewis SE, Groza T, Valentini G, Robinson PN. A Whole-Genome Analysis Framework for Effective Identification of Pathogenic Regulatory Variants in Mendelian Disease. Am J Hum Genet. 2016 Sep 01; 99(3):595-606. PMID: 27569544; PMCID: PMC5011059 [Available on 03/01/17].
      14. Dumontier M, Gray AJG, Marshall MS, Alexiev V, Ansell P, Bader G, Baran J, Bolleman JT, Callahan A, Cruz-Toledo J, Gaudet P, Gombocz EA, Gonzalez-Beltran AN, Groth P, Haendel M, Ito M, Jupp S, Juty N, Katayama T, Kobayashi N, Krishnaswami K, Laibe C, Le Novère N, Lin S, Malone J, Miller M, Mungall C, Rietveld L, Wimalaratne SM, Yamaguchi A. The health care and life sciences community profile for dataset descriptions. PeerJ. 2016; 4:e2331. PMID: 27602295; PMCID: PMC4991880.
      15. McMurry JA, Köhler S, Washington NL, Balhoff JP, Borromeo C, Brush M, Carbon S, Conlin T, Dunn N, Engelstad M, Foster E, Gourdine JP, Jacobsen JO, Keith D, Laraway B, Xuan JN, Shefchek K, Vasilevsky NA, Yuan Z, Lewis SE, Hochheiser H, Groza T, Smedley D, Robinson PN, Mungall C, Haendel MA. Navigating the Phenotype Frontier: The Monarch Initiative. Genetics. 2016 Aug; 203(4):1491-5. PMID: 27516611; PMCID: PMC4981258 [Available on 08/01/17].
      16. Diehl AD, Meehan TF, Bradford YM, Brush MH, Dahdul WM, Dougall DS, He Y, Osumi-Sutherland D, Ruttenberg A, Sarntivijai S, Van Slyke CE, Vasilevsky NA, Haendel MA, Blake JA, Mungall C. The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability. J Biomed Semantics. 2016 Jul 04; 7(1):44. PMID: 27377652; PMCID: PMC4932724.
      17. Bolleman JT, Mungall C, Strozzi F, Baran J, Dumontier M, Bonnal RJ, Buels R, Hoehndorf R, Fujisawa T, Katayama T, Cock PJ. FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation. J Biomed Semantics. 2016; 7:39. PMID: 27296299.
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      18. Xin J, Mark A, Afrasiabi C, Tsueng G, Juchler M, Gopal N, Stupp GS, Putman TE, Ainscough BJ, Griffith OL, Torkamani A, Whetzel PL, Mungall C, Mooney SD, Su AI, Wu C. High-performance web services for querying gene and variant annotation. Genome Biol. 2016 May 06; 17(1):91. PMID: 27154141; PMCID: PMC4858870.
      19. Druzinsky RE, Balhoff JP, Crompton AW, Done J, German RZ, Haendel MA, Herrel A, Herring SW, Lapp H, Mabee PM, Muller HM, Mungall C, Sternberg PW, Van Auken K, Vinyard CJ, Williams SH, Wall CE. Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals. PLoS One. 2016; 11(2):e0149102. PMID: 26870952; PMCID: PMC4752357.
      20. Manda P, Mungall C, Balhoff JP, Lapp H, Vision TJ. INVESTIGATING THE IMPORTANCE OF ANATOMICAL HOMOLOGY FOR CROSS-SPECIES PHENOTYPE COMPARISONS USING SEMANTIC SIMILARITY. Accepted at Pacific Symposium on Biocomputing, 2016. Pac Symp Biocomput. 2016; 21:132-43. PMID: 26776180.
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      21. Thessen AE, Bunker DE, Buttigieg PL, Cooper LD, Dahdul WM, Domisch S, Franz NM, Jaiswal P, Lawrence-Dill CJ, Midford PE, Mungall C, Ramírez MJ, Specht CD, Vogt L, Vos RA, Walls RL, White JW, Zhang G, Deans AR, Huala E, Lewis SE, Mabee PM. Emerging semantics to link phenotype and environment. PeerJ. 2015; 3:e1470. PMID: 26713234; PMCID: PMC4690371.
      22. Bone WP, Washington NL, Buske OJ, Adams DR, Davis J, Draper D, Flynn ED, Girdea M, Godfrey R, Golas G, Groden C, Jacobsen J, Köhler S, Lee EM, Links AE, Markello TC, Mungall C, Nehrebecky M, Robinson PN, Sincan M, Soldatos AG, Tifft CJ, Toro C, Trang H, Valkanas E, Vasilevsky N, Wahl C, Wolfe LA, Boerkoel CF, Brudno M, Haendel MA, Gahl WA, Smedley D. Computational evaluation of exome sequence data using human and model organism phenotypes improves diagnostic efficiency. Genet Med. 2016 Jun; 18(6):608-17. PMID: 26562225; PMCID: PMC4916229.
      23. Robinson PN, Mungall C, Haendel M. Capturing phenotypes for precision medicine. Cold Spring Harb Mol Case Stud. 2015 Oct; 1(1):a000372. PMID: 27148566; PMCID: PMC4850887.
      24. Buske OJ, Schiettecatte F, Hutton B, Dumitriu S, Misyura A, Huang L, Hartley T, Girdea M, Sobreira N, Mungall C, Brudno M. The Matchmaker Exchange API: automating patient matching through the exchange of structured phenotypic and genotypic profiles. Hum Mutat. 2015 Oct; 36(10):922-7. PMID: 26255989; PMCID: PMC4775166 [Available on 10/01/16].
      25. Philippakis AA, Azzariti DR, Beltran S, Brookes AJ, Brownstein CA, Brudno M, Brunner HG, Buske OJ, Carey K, Doll C, Dumitriu S, Dyke SO, den Dunnen JT, Firth HV, Gibbs RA, Girdea M, Gonzalez M, Haendel MA, Hamosh A, Holm IA, Huang L, Hurles ME, Hutton B, Krier JB, Misyura A, Mungall C, Paschall J, Paten B, Robinson PN, Schiettecatte F, Sobreira NL, Swaminathan GJ, Taschner PE, Terry SF, Washington NL, Züchner S, Boycott KM, Rehm HL. The Matchmaker Exchange: a platform for rare disease gene discovery. Hum Mutat. 2015 Oct; 36(10):915-21. PMID: 26295439; PMCID: PMC4610002 [Available on 10/01/16].
      26. Mungall C, Washington NL, Nguyen-Xuan J, Condit C, Smedley D, Köhler S, Groza T, Shefchek K, Hochheiser H, Robinson PN, Lewis SE, Haendel MA. Use of model organism and disease databases to support matchmaking for human disease gene discovery. Hum Mutat. 2015 Oct; 36(10):979-84. PMID: 26269093.
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      27. Groza T, Köhler S, Moldenhauer D, Vasilevsky N, Baynam G, Zemojtel T, Schriml LM, Kibbe WA, Schofield PN, Beck T, Vasant D, Brookes AJ, Zankl A, Washington NL, Mungall C, Lewis SE, Haendel MA, Parkinson H, Robinson PN. The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease. Am J Hum Genet. 2015 Jul 02; 97(1):111-24. PMID: 26119816; PMCID: PMC4572507.
      28. Haendel MA, Vasilevsky N, Brush M, Hochheiser HS, Jacobsen J, Oellrich A, Mungall C, Washington N, Köhler S, Lewis SE, Robinson PN, Smedley D. Disease insights through cross-species phenotype comparisons. Mamm Genome. 2015 Oct; 26(9-10):548-55. PMID: 26092691; PMCID: PMC4602072.
      29. Arner E, Daub CO, Vitting-Seerup K, Andersson R, Lilje B, Drabløs F, Lennartsson A, Rönnerblad M, Hrydziuszko O, Vitezic M, Freeman TC, Alhendi AM, Arner P, Axton R, Baillie JK, Beckhouse A, Bodega B, Briggs J, Brombacher F, Davis M, Detmar M, Ehrlund A, Endoh M, Eslami A, Fagiolini M, Fairbairn L, Faulkner GJ, Ferrai C, Fisher ME, Forrester L, Goldowitz D, Guler R, Ha T, Hara M, Herlyn M, Ikawa T, Kai C, Kawamoto H, Khachigian LM, Klinken SP, Kojima S, Koseki H, Klein S, Mejhert N, Miyaguchi K, Mizuno Y, Morimoto M, Morris KJ, Mummery C, Nakachi Y, Ogishima S, Okada-Hatakeyama M, Okazaki Y, Orlando V, Ovchinnikov D, Passier R, Patrikakis M, Pombo A, Qin XY, Roy S, Sato H, Savvi S, Saxena A, Schwegmann A, Sugiyama D, Swoboda R, Tanaka H, Tomoiu A, Winteringham LN, Wolvetang E, Yanagi-Mizuochi C, Yoneda M, Zabierowski S, Zhang P, Abugessaisa I, Bertin N, Diehl AD, Fukuda S, Furuno M, Harshbarger J, Hasegawa A, Hori F, Ishikawa-Kato S, Ishizu Y, Itoh M, Kawashima T, Kojima M, Kondo N, Lizio M, Meehan TF, Mungall C, Murata M, Nishiyori-Sueki H, Sahin S, Nagao-Sato S, Severin J, de Hoon MJ, Kawai J, Kasukawa T, Lassmann T, Suzuki H, Kawaji H, Summers KM, Wells C. Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells. Science. 2015 Feb 27; 347(6225):1010-4. PMID: 25678556.
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      30. Deans AR, Lewis SE, Huala E, Anzaldo SS, Ashburner M, Balhoff JP, Blackburn DC, Blake JA, Burleigh JG, Chanet B, Cooper LD, Courtot M, Csösz S, Cui H, Dahdul W, Das S, Dececchi TA, Dettai A, Diogo R, Druzinsky RE, Dumontier M, Franz NM, Friedrich F, Gkoutos GV, Haendel M, Harmon LJ, Hayamizu TF, He Y, Hines HM, Ibrahim N, Jackson LM, Jaiswal P, James-Zorn C, Köhler S, Lecointre G, Lapp H, Lawrence CJ, Le Novère N, Lundberg JG, Macklin J, Mast AR, Midford PE, Mikó I, Mungall C, Oellrich A, Osumi-Sutherland D, Parkinson H, Ramírez MJ, Richter S, Robinson PN, Ruttenberg A, Schulz KS, Segerdell E, Seltmann KC, Sharkey MJ, Smith AD, Smith B, Specht CD, Squires RB, Thacker RW, Thessen A, Fernandez-Triana J, Vihinen M, Vize PD, Vogt L, Wall CE, Walls RL, Westerfeld M, Wharton RA, Wirkner CS, Woolley JB, Yoder MJ, Zorn AM, Mabee P. Finding our way through phenotypes. PLoS Biol. 2015 Jan; 13(1):e1002033. PMID: 25562316; PMCID: PMC4285398.
      31. Lizio M, Harshbarger J, Shimoji H, Severin J, Kasukawa T, Sahin S, Abugessaisa I, Fukuda S, Hori F, Ishikawa-Kato S, Mungall C, Arner E, Baillie JK, Bertin N, Bono H, de Hoon M, Diehl AD, Dimont E, Freeman TC, Fujieda K, Hide W, Kaliyaperumal R, Katayama T, Lassmann T, Meehan TF, Nishikata K, Ono H, Rehli M, Sandelin A, Schultes EA, 't Hoen PA, Tatum Z, Thompson M, Toyoda T, Wright DW, Daub CO, Itoh M, Carninci P, Hayashizaki Y, Forrest AR, Kawaji H. Gateways to the FANTOM5 promoter level mammalian expression atlas. Genome Biol. 2015 Jan 05; 16:22. PMID: 25723102; PMCID: PMC4310165.
      32. Dietze H, Berardini TZ, Foulger RE, Hill DP, Lomax J, Osumi-Sutherland D, Roncaglia P, Mungall C. TermGenie - a web-application for pattern-based ontology class generation. J Biomed Semantics. 2014; 5:48. PMID: 25937883; PMCID: PMC4417543.
      33. Kibbe WA, Arze C, Felix V, Mitraka E, Bolton E, Fu G, Mungall C, Binder JX, Malone J, Vasant D, Parkinson H, Schriml LM. Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data. Nucleic Acids Res. 2015 Jan; 43(Database issue):D1071-8. PMID: 25348409; PMCID: PMC4383880.
      34. Thacker RW, Díaz MC, Kerner A, Vignes-Lebbe R, Segerdell E, Haendel MA, Mungall C. The Porifera Ontology (PORO): enhancing sponge systematics with an anatomy ontology. J Biomed Semantics. 2014; 5(1):39. PMID: 25276334; PMCID: PMC4177528.
      35. Ibn-Salem J, Köhler S, Love MI, Chung HR, Huang N, Hurles ME, Haendel M, Washington NL, Smedley D, Mungall C, Lewis SE, Ott CE, Bauer S, Schofield PN, Mundlos S, Spielmann M, Robinson PN. Deletions of chromosomal regulatory boundaries are associated with congenital disease. Genome Biol. 2014 Sep 04; 15(9):423. PMID: 25315429; PMCID: PMC4180961.
      36. Sarntivijai S, Lin Y, Xiang Z, Meehan TF, Diehl AD, Vempati UD, Schürer SC, Pang C, Malone J, Parkinson H, Liu Y, Takatsuki T, Saijo K, Masuya H, Nakamura Y, Brush MH, Haendel MA, Zheng J, Stoeckert CJ, Peters B, Mungall C, Carey TE, States DJ, Athey BD, He Y. CLO: The cell line ontology. J Biomed Semantics. 2014; 5:37. PMID: 25852852; PMCID: PMC4387853.
      37. Dahdul WM, Cui H, Mabee PM, Mungall C, Osumi-Sutherland D, Walls RL, Haendel MA. Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology. J Biomed Semantics. 2014; 5:34. PMID: 25140222; PMCID: PMC4137724.
      38. Chibucos MC, Mungall C, Balakrishnan R, Christie KR, Huntley RP, White O, Blake JA, Lewis SE, Giglio M. Standardized description of scientific evidence using the Evidence Ontology (ECO). Database (Oxford). 2014; 2014. PMID: 25052702; PMCID: PMC4105709.
      39. Alam-Faruque Y, Hill DP, Dimmer EC, Harris MA, Foulger RE, Tweedie S, Attrill H, Howe DG, Thomas SR, Davidson D, Woolf AS, Blake JA, Mungall C, O'Donovan C, Apweiler R, Huntley RP. Representing kidney development using the gene ontology. PLoS One. 2014; 9(6):e99864. PMID: 24941002; PMCID: PMC4062467.
      40. Oellrich A, Koehler S, Washington N. The influence of disease categories on gene candidate predictions from model organism phenotypes. J Biomed Semantics. 2014; 5(Suppl 1 Proceedings of the Bio-Ontologies Spec Interest G):S4. PMID: 25093073; PMCID: PMC4108905.
      41. Huntley RP, Harris MA, Alam-Faruque Y, Blake JA, Carbon S, Dietze H, Dimmer EC, Foulger RE, Hill DP, Khodiyar VK, Lock A, Lomax J, Lovering RC, Mutowo-Meullenet P, Sawford T, Van Auken K, Wood V, Mungall C. A method for increasing expressivity of Gene Ontology annotations using a compositional approach. BMC Bioinformatics. 2014 May 21; 15:155. PMID: 24885854; PMCID: PMC4039540.
      42. Haendel MA, Balhoff JP, Bastian FB, Blackburn DC, Blake JA, Bradford Y, Comte A, Dahdul WM, Dececchi TA, Druzinsky RE, Hayamizu TF, Ibrahim N, Lewis SE, Mabee PM, Niknejad A, Robinson-Rechavi M, Sereno PC, Mungall C. Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon. J Biomed Semantics. 2014; 5:21. PMID: 25009735.
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      43. Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T, Ntini E, Arner E, Valen E, Li K, Schwarzfischer L, Glatz D, Raithel J, Lilje B, Rapin N, Bagger FO, Jørgensen M, Andersen PR, Bertin N, Rackham O, Burroughs AM, Baillie JK, Ishizu Y, Shimizu Y, Furuhata E, Maeda S, Negishi Y, Mungall C, Meehan TF, Lassmann T, Itoh M, Kawaji H, Kondo N, Kawai J, Lennartsson A, Daub CO, Heutink P, Hume DA, Jensen TH, Suzuki H, Hayashizaki Y, Müller F, Forrest ARR, Carninci P, Rehli M, Sandelin A. An atlas of active enhancers across human cell types and tissues. Nature. 2014 Mar 27; 507(7493):455-461. PMID: 24670763.
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      44. A promoter-level mammalian expression atlas. Nature. 2014 Mar 27; 507(7493):462-70. PMID: 24670764; PMCID: PMC4529748.
      45. Buttigieg PL, Morrison N, Smith B, Mungall C, Lewis SE. The environment ontology: contextualising biological and biomedical entities. J Biomed Semantics. 2013 Dec 11; 4(1):43. PMID: 24330602; PMCID: PMC3904460.
      46. Köhler S, Doelken SC, Mungall C, Bauer S, Firth HV, Bailleul-Forestier I, Black GC, Brown DL, Brudno M, Campbell J, FitzPatrick DR, Eppig JT, Jackson AP, Freson K, Girdea M, Helbig I, Hurst JA, Jähn J, Jackson LG, Kelly AM, Ledbetter DH, Mansour S, Martin CL, Moss C, Mumford A, Ouwehand WH, Park SM, Riggs ER, Scott RH, Sisodiya S, Van Vooren S, Wapner RJ, Wilkie AO, Wright CF, Vulto-van Silfhout AT, de Leeuw N, de Vries BB, Washingthon NL, Smith CL, Westerfield M, Schofield P, Ruef BJ, Gkoutos GV, Haendel M, Smedley D, Lewis SE, Robinson PN. The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. Nucleic Acids Res. 2014 Jan; 42(Database issue):D966-74. PMID: 24217912; PMCID: PMC3965098.
      47. Robinson PN, Köhler S, Oellrich A. Improved exome prioritization of disease genes through cross-species phenotype comparison. Genome Res. 2014 Feb; 24(2):340-8. PMID: 24162188; PMCID: PMC3912424.
      48. Druzinsky R, Mungall C, Haendel M, Lapp H, Mabee P. What is an anatomy ontology? Anat Rec (Hoboken). 2013 Dec; 296(12):1797-9. PMID: 24127438.
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      49. Roncaglia P, Martone ME, Hill DP, Berardini TZ, Foulger RE, Imam FT, Drabkin H, Mungall C, Lomax J. The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments. J Biomed Semantics. 2013 Oct 07; 4(1):20. PMID: 24093723; PMCID: PMC3852282.
      50. Meehan TF, Vasilevsky NA, Mungall C, Dougall DS, Haendel MA, Blake JA, Diehl AD. Ontology based molecular signatures for immune cell types via gene expression analysis. BMC Bioinformatics. 2013 Aug 30; 14:263. PMID: 24004649; PMCID: PMC3844401.
      51. Hill DP, Adams N, Bada M, Batchelor C, Berardini TZ, Dietze H, Drabkin HJ, Ennis M, Foulger RE, Harris MA, Hastings J, Kale NS, de Matos P, Mungall C, Owen G, Roncaglia P, Steinbeck C, Turner S, Lomax J. Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology. BMC Genomics. 2013 Jul 29; 14:513. PMID: 23895341; PMCID: PMC3733925.
      52. Maynard SM, Mungall C, Lewis SE, Imam FT, Martone ME. A knowledge based approach to matching human neurodegenerative disease and animal models. Front Neuroinform. 2013; 7:7. PMID: 23717278; PMCID: PMC3653101.
      53. Smedley D, Oellrich A, Köhler S, Ruef B. PhenoDigm: analyzing curated annotations to associate animal models with human diseases. Database (Oxford). 2013; 2013:bat025. PMID: 23660285; PMCID: PMC3649640.
      54. Köhler S, Doelken SC, Ruef BJ, Bauer S, Washington N, Westerfield M, Gkoutos G, Schofield P, Smedley D, Lewis SE, Robinson PN, Mungall C. Construction and accessibility of a cross-species phenotype ontology along with gene annotations for biomedical research. F1000Res. 2013; 2:30. PMID: 24358873; PMCID: PMC3799545.
      55. Aranguren ME, Fernández-Breis JT, Mungall C, Antezana E, González AR, Wilkinson MD. OPPL-Galaxy, a Galaxy tool for enhancing ontology exploitation as part of bioinformatics workflows. J Biomed Semantics. 2013 Jan 04; 4(1):2. PMID: 23286517; PMCID: PMC3643862.
      56. Dahdul WM, Balhoff JP, Blackburn DC, Diehl AD, Haendel MA, Hall BK, Lapp H, Lundberg JG, Mungall C, Ringwald M, Segerdell E, Van Slyke CE, Vickaryous MK, Westerfield M, Mabee PM. A unified anatomy ontology of the vertebrate skeletal system. PLoS One. 2012; 7(12):e51070. PMID: 23251424; PMCID: PMC3519498.
      57. Cooper L, Walls RL, Elser J, Gandolfo MA, Stevenson DW, Smith B, Preece J, Athreya B, Mungall C, Rensing S, Hiss M, Lang D, Reski R, Berardini TZ, Li D, Huala E, Schaeffer M, Menda N, Arnaud E, Shrestha R, Yamazaki Y, Jaiswal P. The plant ontology as a tool for comparative plant anatomy and genomic analyses. Plant Cell Physiol. 2013 Feb; 54(2):e1. PMID: 23220694; PMCID: PMC3583023.
      58. Gene Ontology annotations and resources. Nucleic Acids Res. 2013 Jan; 41(Database issue):D530-5. PMID: 23161678; PMCID: PMC3531070.
      59. Doelken SC, Köhler S, Mungall C, Gkoutos GV, Ruef BJ, Smith C, Smedley D, Bauer S, Klopocki E, Schofield PN, Westerfield M, Robinson PN, Lewis SE. Phenotypic overlap in the contribution of individual genes to CNV pathogenicity revealed by cross-species computational analysis of single-gene mutations in humans, mice and zebrafish. Dis Model Mech. 2013 Mar; 6(2):358-72. PMID: 23104991; PMCID: PMC3597018.
      60. Walls RL, Athreya B, Cooper L, Elser J, Gandolfo MA, Jaiswal P, Mungall C, Preece J, Rensing S, Smith B, Stevenson DW. Ontologies as integrative tools for plant science. Am J Bot. 2012 Aug; 99(8):1263-75. PMID: 22847540; PMCID: PMC3492881.
      61. Chen CK, Mungall C, Gkoutos GV, Doelken SC, Köhler S, Ruef BJ, Smith C, Westerfield M, Robinson PN, Lewis SE, Schofield PN, Smedley D. MouseFinder: Candidate disease genes from mouse phenotype data. Hum Mutat. 2012 May; 33(5):858-66. PMID: 22331800; PMCID: PMC3327758.
      62. Osumi-Sutherland D, Reeve S, Mungall C, Neuhaus F, Ruttenberg A, Jefferis GS, Armstrong JD. A strategy for building neuroanatomy ontologies. Bioinformatics. 2012 May 01; 28(9):1262-9. PMID: 22402613.
        View in: PubMed
      63. Thomas PD, Wood V, Mungall C, Lewis SE, Blake JA. On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report. PLoS Comput Biol. 2012; 8(2):e1002386. PMID: 22359495; PMCID: PMC3280971.
      64. Mungall C, Torniai C, Gkoutos GV, Lewis SE, Haendel MA. Uberon, an integrative multi-species anatomy ontology. Genome Biol. 2012 Jan 31; 13(1):R5. PMID: 22293552.
        View in: PubMed
      65. Köhler S, Bauer S, Mungall C, Carletti G, Smith CL, Schofield P, Gkoutos GV, Robinson PN. Improving ontologies by automatic reasoning and evaluation of logical definitions. BMC Bioinformatics. 2011 Oct 27; 12:418. PMID: 22032770; PMCID: PMC3224779.
      66. Tirmizi SH, Aitken S, Moreira DA, Mungall C, Sequeda J, Shah NH, Miranker DP. Mapping between the OBO and OWL ontology languages. J Biomed Semantics. 2011 Mar 07; 2 Suppl 1:S3. PMID: 21388572; PMCID: PMC3105495.
      67. Meehan TF, Masci AM, Abdulla A, Cowell LG, Blake JA, Mungall C, Diehl AD. Logical development of the cell ontology. BMC Bioinformatics. 2011 Jan 05; 12:6. PMID: 21208450; PMCID: PMC3024222.
      68. Antezana E, Venkatesan A, Mungall C, Mironov V, Kuiper M. ONTO-ToolKit: enabling bio-ontology engineering via Galaxy. BMC Bioinformatics. 2010 Dec 21; 11 Suppl 12:S8. PMID: 21210987; PMCID: PMC3040534.
      69. Deegan née Clark JI, Dimmer EC, Mungall C. Formalization of taxon-based constraints to detect inconsistencies in annotation and ontology development. BMC Bioinformatics. 2010 Oct 25; 11:530. PMID: 20973947; PMCID: PMC3098089.
      70. Mungall C, Batchelor C, Eilbeck K. Evolution of the Sequence Ontology terms and relationships. J Biomed Inform. 2011 Feb; 44(1):87-93. PMID: 20226267; PMCID: PMC3052763.
      71. Mungall C, Bada M, Berardini TZ, Deegan J, Ireland A, Harris MA, Hill DP, Lomax J. Cross-product extensions of the Gene Ontology. J Biomed Inform. 2011 Feb; 44(1):80-6. PMID: 20152934; PMCID: PMC2910209.
      72. Diehl AD, Augustine AD, Blake JA, Cowell LG, Gold ES, Gondré-Lewis TA, Masci AM, Meehan TF, Morel PA, Nijnik A, Peters B, Pulendran B, Scheuermann RH, Yao QA, Zand MS, Mungall C. Hematopoietic cell types: prototype for a revised cell ontology. J Biomed Inform. 2011 Feb; 44(1):75-9. PMID: 20123131; PMCID: PMC2892030.
      73. Alterovitz G, Xiang M, Hill DP, Lomax J, Liu J, Cherkassky M, Dreyfuss J, Mungall C, Harris MA, Dolan ME, Blake JA, Ramoni MF. Ontology engineering. Nat Biotechnol. 2010 Feb; 28(2):128-30. PMID: 20139945; PMCID: PMC4829499.
      74. Mungall C, Gkoutos GV, Smith CL, Haendel MA, Lewis SE, Ashburner M. Integrating phenotype ontologies across multiple species. Genome Biol. 2010 Jan 08; 11(1):R2. PMID: 20064205; PMCID: PMC2847714.
      75. Washington NL, Haendel MA, Mungall C, Ashburner M, Westerfield M, Lewis SE. Linking human diseases to animal models using ontology-based phenotype annotation. PLoS Biol. 2009 Nov; 7(11):e1000247. PMID: 19956802; PMCID: PMC2774506.
      76. Karp DR, Marthandan N, Marsh SG, Ahn C, Arnett FC, Deluca DS, Diehl AD, Dunivin R, Eilbeck K, Feolo M, Guidry PA, Helmberg W, Lewis S, Mayes MD, Mungall C, Natale DA, Peters B, Petersdorf E, Reveille JD, Smith B, Thomson G, Waller MJ, Scheuermann RH. Novel sequence feature variant type analysis of the HLA genetic association in systemic sclerosis. Hum Mol Genet. 2010 Feb 15; 19(4):707-19. PMID: 19933168; PMCID: PMC2807365.
      77. Hancock JM, Mallon AM, Beck T, Gkoutos GV, Mungall C, Schofield PN. Mouse, man, and meaning: bridging the semantics of mouse phenotype and human disease. Mamm Genome. 2009 Aug; 20(8):457-61. PMID: 19649761; PMCID: PMC2759022.
      78. Skinner ME, Uzilov AV, Stein LD, Mungall C, Holmes IH. JBrowse: a next-generation genome browser. Genome Res. 2009 Sep; 19(9):1630-8. PMID: 19570905; PMCID: PMC2752129.
      79. Schober D, Smith B, Lewis SE, Kusnierczyk W, Lomax J, Mungall C, Taylor CF, Rocca-Serra P, Sansone SA. Survey-based naming conventions for use in OBO Foundry ontology development. BMC Bioinformatics. 2009 Apr 27; 10:125. PMID: 19397794; PMCID: PMC2684543.
      80. Masci AM, Arighi CN, Diehl AD, Lieberman AE, Mungall C, Scheuermann RH, Smith B, Cowell LG. An improved ontological representation of dendritic cells as a paradigm for all cell types. BMC Bioinformatics. 2009 Feb 25; 10:70. PMID: 19243617; PMCID: PMC2662812.
      81. Gkoutos GV, Mungall C, Dolken S, Ashburner M, Lewis S, Hancock J, Schofield P, Kohler S, Robinson PN. Entity/quality-based logical definitions for the human skeletal phenome using PATO. Conf Proc IEEE Eng Med Biol Soc. 2009; 2009:7069-72. PMID: 19964203; PMCID: PMC3398700.
      82. Carbon S, Ireland A, Mungall C, Shu S, Marshall B, Lewis S. AmiGO: online access to ontology and annotation data. Bioinformatics. 2009 Jan 15; 25(2):288-9. PMID: 19033274; PMCID: PMC2639003.
      83. Yandell M, Moore B, Salas F, Mungall C, MacBride A, White C, Reese MG. Genome-wide analysis of human disease alleles reveals that their locations are correlated in paralogous proteins. PLoS Comput Biol. 2008 Nov; 4(11):e1000218. PMID: 18989397; PMCID: PMC2565504.
      84. Pfeiffer BD, Jenett A, Hammonds AS, Ngo TT, Misra S, Murphy C, Scully A, Carlson JW, Wan KH, Laverty TR, Mungall C, Svirskas R, Kadonaga JT, Doe CQ, Eisen MB, Celniker SE, Rubin GM. Tools for neuroanatomy and neurogenetics in Drosophila. Proc Natl Acad Sci U S A. 2008 Jul 15; 105(28):9715-20. PMID: 18621688; PMCID: PMC2447866.
      85. Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall C. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol. 2007 Nov; 25(11):1251-5. PMID: 17989687; PMCID: PMC2814061.
      86. Mungall C, Emmert DB. A Chado case study: an ontology-based modular schema for representing genome-associated biological information. Bioinformatics. 2007 Jul 01; 23(13):i337-46. PMID: 17646315.
        View in: PubMed
      87. Smith CD, Shu S, Mungall C, Karpen GH. The Release 5.1 annotation of Drosophila melanogaster heterochromatin. Science. 2007 Jun 15; 316(5831):1586-91. PMID: 17569856; PMCID: PMC2819280.
      88. Mabee PM, Ashburner M, Cronk Q, Gkoutos GV, Haendel M, Segerdell E, Mungall C, Westerfield M. Phenotype ontologies: the bridge between genomics and evolution. Trends Ecol Evol. 2007 Jul; 22(7):345-50. PMID: 17416439.
        View in: PubMed
      89. Yandell M, Mungall C, Smith C, Prochnik S, Kaminker J, Hartzell G, Lewis S, Rubin GM. Large-scale trends in the evolution of gene structures within 11 animal genomes. PLoS Comput Biol. 2006 Mar; 2(3):e15. PMID: 16518452; PMCID: PMC1386723.
      90. Rubin DL, Lewis SE, Mungall C, Misra S, Westerfield M, Ashburner M, Sim I, Chute CG, Solbrig H, Storey MA, Smith B, Day-Richter J, Noy NF, Musen MA. National Center for Biomedical Ontology: advancing biomedicine through structured organization of scientific knowledge. OMICS. 2006; 10(2):185-98. PMID: 16901225.
        View in: PubMed
      91. Eilbeck K, Lewis SE, Mungall C, Yandell M, Stein L, Durbin R, Ashburner M. The Sequence Ontology: a tool for the unification of genome annotations. Genome Biol. 2005; 6(5):R44. PMID: 15892872; PMCID: PMC1175956.
      92. Smith B, Ceusters W, Klagges B, Köhler J, Kumar A, Lomax J, Mungall C, Neuhaus F, Rector AL, Rosse C. Relations in biomedical ontologies. Genome Biol. 2005; 6(5):R46. PMID: 15892874; PMCID: PMC1175958.
      93. Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R, Eilbeck K, Lewis S, Marshall B, Mungall C, Richter J, Rubin GM, Blake JA, Bult C, Dolan M, Drabkin H, Eppig JT, Hill DP, Ni L, Ringwald M, Balakrishnan R, Cherry JM, Christie KR, Costanzo MC, Dwight SS, Engel S, Fisk DG, Hirschman JE, Hong EL, Nash RS, Sethuraman A, Theesfeld CL, Botstein D, Dolinski K, Feierbach B, Berardini T, Mundodi S, Rhee SY, Apweiler R, Barrell D, Camon E, Dimmer E, Lee V, Chisholm R, Gaudet P, Kibbe W, Kishore R, Schwarz EM, Sternberg P, Gwinn M, Hannick L, Wortman J, Berriman M, Wood V, de la Cruz N, Tonellato P, Jaiswal P, Seigfried T, White R. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res. 2004 Jan 01; 32(Database issue):D258-61. PMID: 14681407; PMCID: PMC308770.
      94. Mungall C. Obol: integrating language and meaning in bio-ontologies. Comp Funct Genomics. 2004; 5(6-7):509-20. PMID: 18629143; PMCID: PMC2447432.
      95. Ashburner M, Mungall C, Lewis SE. Ontologies for biologists: a community model for the annotation of genomic data. Cold Spring Harb Symp Quant Biol. 2003; 68:227-35. PMID: 15338622.
        View in: PubMed
      96. Hoskins RA, Smith CD, Carlson JW, Carvalho AB, Halpern A, Kaminker JS, Kennedy C, Mungall C, Sullivan BA, Sutton GG, Yasuhara JC, Wakimoto BT, Myers EW, Celniker SE, Rubin GM, Karpen GH. Heterochromatic sequences in a Drosophila whole-genome shotgun assembly. Genome Biol. 2002; 3(12):RESEARCH0085. PMID: 12537574; PMCID: PMC151187.
      97. Misra S, Crosby MA, Mungall C, Matthews BB, Campbell KS, Hradecky P, Huang Y, Kaminker JS, Millburn GH, Prochnik SE, Smith CD, Tupy JL, Whitfied EJ, Bayraktaroglu L, Berman BP, Bettencourt BR, Celniker SE, de Grey AD, Drysdale RA, Harris NL, Richter J, Russo S, Schroeder AJ, Shu SQ, Stapleton M, Yamada C, Ashburner M, Gelbart WM, Rubin GM, Lewis SE. Annotation of the Drosophila melanogaster euchromatic genome: a systematic review. Genome Biol. 2002; 3(12):RESEARCH0083. PMID: 12537572; PMCID: PMC151185.
      98. Bergman CM, Pfeiffer BD, Rincón-Limas DE, Hoskins RA, Gnirke A, Mungall C, Wang AM, Kronmiller B, Pacleb J, Park S, Stapleton M, Wan K, George RA, de Jong PJ, Botas J, Rubin GM, Celniker SE. Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome. Genome Biol. 2002; 3(12):RESEARCH0086. PMID: 12537575.
        View in: PubMed
      99. Mungall C, Misra S, Berman BP, Carlson J, Frise E, Harris N, Marshall B, Shu S, Kaminker JS, Prochnik SE, Smith CD, Smith E, Tupy JL, Wiel C, Rubin GM, Lewis SE. An integrated computational pipeline and database to support whole-genome sequence annotation. Genome Biol. 2002; 3(12):RESEARCH0081. PMID: 12537570; PMCID: PMC151183.
      100. Lewis SE, Searle SM, Harris N, Gibson M, Lyer V, Richter J, Wiel C, Bayraktaroglu L, Birney E, Crosby MA, Kaminker JS, Matthews BB, Prochnik SE, Smithy CD, Tupy JL, Rubin GM, Misra S, Mungall C, Clamp ME. Apollo: a sequence annotation editor. Genome Biol. 2002; 3(12):RESEARCH0082. PMID: 12537571; PMCID: PMC151184.
      101. Gardner MJ, Hall N, Fung E, White O, Berriman M, Hyman RW, Carlton JM, Pain A, Nelson KE, Bowman S, Paulsen IT, James K, Eisen JA, Rutherford K, Salzberg SL, Craig A, Kyes S, Chan MS, Nene V, Shallom SJ, Suh B, Peterson J, Angiuoli S, Pertea M, Allen J, Selengut J, Haft D, Mather MW, Vaidya AB, Martin DM, Fairlamb AH, Fraunholz MJ, Roos DS, Ralph SA, McFadden GI, Cummings LM, Subramanian GM, Mungall C, Venter JC, Carucci DJ, Hoffman SL, Newbold C, Davis RW, Fraser CM, Barrell B. Genome sequence of the human malaria parasite Plasmodium falciparum. Nature. 2002 Oct 03; 419(6906):498-511. PMID: 12368864; PMCID: PMC3836256.
      102. Stein LD, Mungall C, Shu S, Caudy M, Mangone M, Day A, Nickerson E, Stajich JE, Harris TW, Arva A, Lewis S. The generic genome browser: a building block for a model organism system database. Genome Res. 2002 Oct; 12(10):1599-610. PMID: 12368253; PMCID: PMC187535.
      103. Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C, Fuellen G, Gilbert JG, Korf I, Lapp H, Lehväslaiho H, Matsalla C, Mungall C, Osborne BI, Pocock MR, Schattner P, Senger M, Stein LD, Stupka E, Wilkinson MD, Birney E. The Bioperl toolkit: Perl modules for the life sciences. Genome Res. 2002 Oct; 12(10):1611-8. PMID: 12368254; PMCID: PMC187536.
      104. Hu J, Mungall C, Law A, Papworth R, Nelson JP, Brown A, Simpson I, Leckie S, Burt DW, Hillyard AL, Archibald AL. The ARKdb: genome databases for farmed and other animals. Nucleic Acids Res. 2001 Jan 01; 29(1):106-10. PMID: 11125062; PMCID: PMC29807.
      105. Burnatowska-Hledin M, Zhao P, Capps B, Poel A, Parmelee K, Mungall C, Sharangpani A, Listenberger L. VACM-1, a cullin gene family member, regulates cellular signaling. Am J Physiol Cell Physiol. 2000 Jul; 279(1):C266-73. PMID: 10898738.
        View in: PubMed
      106. Rubin GM, Yandell MD, Wortman JR, Gabor Miklos GL, Nelson CR, Hariharan IK, Fortini ME, Li PW, Apweiler R, Fleischmann W, Cherry JM, Henikoff S, Skupski MP, Misra S, Ashburner M, Birney E, Boguski MS, Brody T, Brokstein P, Celniker SE, Chervitz SA, Coates D, Cravchik A, Gabrielian A, Galle RF, Gelbart WM, George RA, Goldstein LS, Gong F, Guan P, Harris NL, Hay BA, Hoskins RA, Li J, Li Z, Hynes RO, Jones SJ, Kuehl PM, Lemaitre B, Littleton JT, Morrison DK, Mungall C, O'Farrell PH, Pickeral OK, Shue C, Vosshall LB, Zhang J, Zhao Q, Zheng XH, Lewis S. Comparative genomics of the eukaryotes. Science. 2000 Mar 24; 287(5461):2204-15. PMID: 10731134; PMCID: PMC2754258.
      107. Hu J, Mungall C, Nicholson D, Archibald AL. Design and implementation of a CORBA-based genome mapping system prototype. Bioinformatics. 1998; 14(2):112-20. PMID: 9545442.
        View in: PubMed

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